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FSL  August 2009

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Subject:

Re: How to temporarily disable SGE in FEAT

From:

wolf zinke <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 13 Aug 2009 12:37:31 +0200

Content-Type:

text/plain

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text/plain (97 lines)

Hi Steve,

You have been right, it was my fault, because I misinterpreted something 
in the fsl_sub file and made a change that was causing the problem.
There is a part where the SGE initialisation is done:

[...]
METHOD=SGE
if [ "x$SGE_ROOT" = "x" ] ; then
    if [ -f /usr/local/share/sge/default/common/settings.sh ] ; then
    . /usr/local/share/sge/default/common/settings.sh
    elif [ -f /usr/local/sge/default/common/settings.sh ] ; then
    . /usr/local/sge/default/common/settings.sh
    else
    METHOD=NONE
    fi
fi
[...]

I assumed that I have to set the file for my environment 
('/usr/sge/default/common/settings.sh'), and of course this was setting 
again the variable SGE_ROOT. So I guess that this kind of problem I 
introduced could occur whenever someone sets up SGE with the paths as 
specified here. Would it not be more reliable to check whether the 
variable SGE_ROOT is set and decide based on this to use SGE?
Anyway, now everything seems to work fine again and I am happy. Sorry 
for causing this problem by myself.

wolf



Steve Smith wrote:
> Yes - you could - though I have never seen this problem before - for 
> me, unsetting SGE_ROOT always works - maybe you have a locally 
> modified fsl_sub that doesn't obey this?
> Cheers.
>
>
> On 13 Aug 2009, at 03:58, Xue, Feng wrote:
>
>> try modify $FSLDIR/bin/fsl_sub and in method config section, set
>> METHOD=NONE below the outer "fi" line
>>
>> On Thu, Aug 13, 2009 at 3:19 AM, wolf 
>> zinke<[log in to unmask]> wrote:
>>> Hi,
>>>
>>> I try desperately to run FEAT without using SGE, but I have not 
>>> found a good
>>> solution.I tried to use "unset SGE_ROOT" or "SGE_ROOT='';export 
>>> SGE_ROOT"
>>> before calling "feat some.fsf" from the same shell. But for some 
>>> reason it
>>> always submits all jobs to SGE. I want to run a set of feat analysis 
>>> single
>>> threaded because otherwise I am running out of RAM pretty fast. It 
>>> would be
>>> great to have a simple flag withing Feat that sets whether to use or 
>>> not to
>>> use SGE facilities via fsl_sub. Is there such an reliable option 
>>> already
>>> available?
>>>
>>> Thanks for all the help,
>>> wolf
>>>
>>
>>
>>
>> -- 
>> Best Regards
>>
>>
>> National Key Laboratory of Cognitive Neuroscience and Learning
>> Beijing Normal University
>> Beijing, China. 100875
>> Tel: +86-13810154455
>> web: http://psychbrain.bnu.edu.cn
>> ==============================================
>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
>> telnet://bbs.mdjs.org
>> http://bbs.mdjs.org
>>
>
>
> --------------------------------------------------------------------------- 
>
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> --------------------------------------------------------------------------- 
>

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